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Bioinformatics Advance Access originally published online on April 1, 2004
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Bioinformatics 20(13) © Oxford University Press 2004; all rights reserved.

Molecular Genetics Information System (MOLGENIS): alternatives in developing local experimental genomics databases

Morris A. Swertz 1,*, E. O. (Bert) de Brock 1,2, Sacha A. F. T. van Hijum 3, Anne de Jong 3, Girbe Buist 3, Richard J. S. Baerends 3, Jan Kok 3, Oscar P. Kuipers 3 and Ritsert C. Jansen 1

1 Groningen Bioinformatics Center (GBIC), Faculty of Medical Sciences and Faculty of Mathematics and Natural Sciences and 2 Faculty of Management and Organization, University of Groningen, P.O. Box 800, NL-9700 AV Groningen, The Netherlands and 3 Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, P.O. Box 14, NL-9750 AA Haren, The Netherlands

Received on October 15, 2004; revised on January 5, 2004; accepted on March 8, 2004
Advance Access Publication April 1, 2004

Motivation: Genomic research laboratories need adequate infrastructure to support management of their data production and research workflow. But what makes infrastructure adequate? A lack of appropriate criteria makes any decision on buying or developing a system difficult. Here, we report on the decision process for the case of a molecular genetics group establishing a microarray laboratory.

Results: Five typical requirements for experimental genomics database systems were identified: (i) evolution ability to keep up with the fast developing genomics field; (ii) a suitable data model to deal with local diversity; (iii) suitable storage of data files in the system; (iv) easy exchange with other software; and (v) low maintenance costs. The computer scientists and the researchers of the local microarray laboratory considered alternative solutions for these five requirements and chose the following options: (i) use of automatic code generation; (ii) a customized data model based on standards; (iii) storage of datasets as black boxes instead of decomposing them in database tables; (iv) loosely linking to other programs for improved flexibility; and (v) a low-maintenance web-based user interface. Our team evaluated existing microarray databases and then decided to build a new system, Molecular Genetics Information System (MOLGENIS), implemented using code generation in a period of three months. This case can provide valuable insights and lessons to both software developers and a user community embarking on large-scale genomic projects.

Availability: http://www.molgenis.nl

Contact: m.a.swertz{at}cs.rug.nl

* To whom correspondence should be addressed.


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